ArticleBMC bioinformatics2011
SIGNATURE: a workbench for gene expression signature analysis.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- HIF-1-mediated PPME1 expression promotes breast cancer progression via AKT activation and β-catenin recruitment.The Journal of clinical investigation · 2026Article
- Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities.Chemical research in toxicology · 2022Review
- AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation.The FEBS journal · 2022Article
- Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.Genome biology · 2022Article
- Predicting clinical response to everolimus in ER+ breast cancers using machine-learning.Frontiers in molecular biosciences · 2022Article
- Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer.Nature communications · 2021Article
- Article
- signatureSearch: environment for gene expression signature searching and functional interpretation.Nucleic acids research · 2020Article
- Merging microarray studies to identify a common gene expression signature to several structural heart diseases.BioData mining · 2020Article
- Nrf2 and SQSTM1/p62 jointly contribute to mesenchymal transition and invasion in glioblastoma.Oncogene · 2019Article
- Targeting the Interplay between Epithelial-to-Mesenchymal-Transition and the Immune System for Effective Immunotherapy.Cancers · 2019Review
- Contributions of the RhoA guanine nucleotide exchange factor Net1 to polyoma middle T antigen-mediated mammary gland tumorigenesis and metastasis.Breast cancer research : BCR · 2018Article
- Planning bioinformatics workflows using an expert system.Bioinformatics (Oxford, England) · 2017Article
- Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd.Nature communications · 2016Article
- ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate.PLoS genetics · 2015Article
- PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links.Frontiers in bioengineering and biotechnology · 2015Article
- Utilization of the Eμ-Myc mouse to model heterogeneity of therapeutic response.Molecular cancer therapeutics · 2014Article
- An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer.Nature genetics · 2014Article
- High CD49f expression is associated with osteosarcoma tumor progression: a study using patient-derived primary cell cultures.Cancer medicine · 2014Article
- A signature of epithelial-mesenchymal plasticity and stromal activation in primary tumor modulates late recurrence in breast cancer independent of disease subtype.Breast cancer research : BCR · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundThe biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise.
resultsWe have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access.
conclusionsSIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.